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## G

G - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
G_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
GAMCOF - Static variable in class org.metaqtl.numrec.NumericalUtilities
gammln(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
gammp(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
gauss(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  This routine returns the value at x of the normal centered gaussian density.
gcf(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
gen - Variable in class org.metaqtl.Qtl.QTLCross
  The number of generations.
gen - Static variable in class org.thalia.bio.util.BioCrossTypes
generalHelp() - Static method in class org.metaqtl.main.MetaMain
generalUsage() - Static method in class org.metaqtl.main.MetaMain
GeneticMap - Class in org.thalia.bio.entity
  Class Description Here
GeneticMap() - Constructor for class org.thalia.bio.entity.GeneticMap
GeneticMap(String, IBioEntity) - Constructor for class org.thalia.bio.entity.GeneticMap
GeneticMap(String) - Constructor for class org.thalia.bio.entity.GeneticMap
GeneticMapBean - Class in org.thalia.bio.entity.bean
  Class Description Here
GeneticMapBean() - Constructor for class org.thalia.bio.entity.bean.GeneticMapBean
GeneticMapBeanAdapter - Class in org.thalia.bio.entity.adapter
  Class Description Here
GeneticMapBeanAdapter() - Constructor for class org.thalia.bio.entity.adapter.GeneticMapBeanAdapter
GeneticMapProperties - Class in org.metaqtl.util
  General comments must be added here.
GeneticMapProperties() - Constructor for class org.metaqtl.util.GeneticMapProperties
GENOME - Static variable in interface org.thalia.bio.IBioEntityTypes
  The integer code for Genome entity
getAdjacentTable() - Method in class org.metaqtl.ChromCluster.ClusterGraph
getAllele(String) - Method in class org.thalia.bio.entity.AlleleContainer
getAllele(String) - Method in interface org.thalia.bio.IBioLocus
getAlleleNumber() - Method in class org.thalia.bio.entity.AlleleContainer
getAlleleNumber() - Method in interface org.thalia.bio.IBioLocus
getBestClustering(int) - Method in class org.metaqtl.MetaQtlResult
  This methods returns the best models for each criterion defined to select the optimal number of clusters per trait.
getBestModel(int) - Method in class org.metaqtl.MetaQtlAnalysis
  This methods returns the best models for each criterion defined to select the optimal number of clusters per chromosome per trait.
getBestResult(EMResult[], int) - Static method in class org.metaqtl.EMCriteria
  For the given criterion `criterion` this methods looks into the array of `EMResult` and find the model which is optimal.
getBestResult(EMResult[], int, int) - Static method in class org.metaqtl.EMCriteria
getBestResult(EMResult[], String) - Static method in class org.metaqtl.EMCriteria
getBestResult(EMResult[], int, String) - Static method in class org.metaqtl.EMCriteria
getBioAdapter() - Method in class org.thalia.bio.entity.BioEntityCollection
getBioAdapter() - Method in class org.thalia.bio.entity.GeneticMap
getBioAdapter() - Method in class org.thalia.bio.entity.Individual
getBioAdapter() - Method in class org.thalia.bio.entity.LGroup
getBioAdapter() - Method in class org.thalia.bio.entity.Marker
getBioAdapter() - Method in class org.thalia.bio.entity.Ontology
getBioAdapter() - Method in class org.thalia.bio.entity.OntologyTerm
getBioAdapter() - Method in class org.thalia.bio.entity.Population
getBioAdapter() - Method in class org.thalia.bio.entity.QTL
getBioAdapter() - Method in interface org.thalia.bio.IBioAdaptable
getCard() - Method in class org.metaqtl.TreeNode
getCentroid(double[], double[]) - Method in class org.metaqtl.TreeNode
getChildren() - Method in class org.metaqtl.TreeNode
getChildrenTerm() - Method in class org.thalia.bio.entity.OntologyTerm
getChildrenTerm() - Method in interface org.thalia.bio.IBioOntologyTerm
  Returns the children if the term has chilren, null otherwise.
getChromAxe() - Method in class org.metaqtl.graph.ChromLayer
  Return the axe of the chromosome.
getChromAxe() - Method in class org.metaqtl.graph.ChromShape
getChromAxe() - Method in class org.metaqtl.graph.QtlPartitionLayer
getChromByNames(Chromosome[], String[]) - Static method in class org.metaqtl.main.MetaMain
getChromGraph(Chromosome[], boolean, int, IBioOntology, MetaQtlAnalysis) - Static method in class org.metaqtl.main.MetaMain
getChromIdx(String) - Method in class org.metaqtl.MetaQtlAnalysis
getChromNames() - Method in class org.metaqtl.MetaQtlModel
  Returns the names of the chromosomes.
getChromosomeName(String) - Method in class org.metaqtl.MapCluster
  This method returns the name of the chromosome from the given name.
getChromWidth() - Method in class org.metaqtl.graph.ChromLayer
getChromWidth() - Method in class org.metaqtl.graph.ChromShape
getClusterByNames(ChromCluster[], String[]) - Static method in class org.metaqtl.main.MetaMain
getClustering(int) - Method in class org.metaqtl.MetaQtlResult
  Returns the Qtl clustering result with `k` clusters.
getClusterMembers() - Method in class org.metaqtl.ChromCluster
  This method returns the members of the cluster as an array of `Chromosomes`.
getClusters() - Method in class org.metaqtl.MapCluster
  Returns the chromosome clusters.
getCMrkTotalNumbers() - Method in class org.metaqtl.ChromCluster
getCommonMarkerPaths(ChromLayer) - Method in class org.metaqtl.graph.ChromLayer
getCommonMarkerPoints(ChromLayer) - Method in class org.metaqtl.graph.ChromLayer
getCopy() - Method in class org.metaqtl.Qtl
  Returns a copy of the QTL.
getCopy() - Method in class org.metaqtl.Qtl.QTLCross
getCopy() - Method in class org.metaqtl.Qtl.QTLProj
getCopy() - Method in class org.metaqtl.Qtl.QTLStats
getCopy() - Method in class org.metaqtl.Qtl.QTLSupport
getCopy() - Method in class org.metaqtl.Qtl.QTLTrait
getCritDelta(String, int[]) - Method in class org.metaqtl.MetaQtlResult
getCriteria() - Static method in class org.metaqtl.EMCriteria
  Returns an iterator on the criteria
getCriteria() - Method in class org.metaqtl.MetaQtlResult
getCriterion(int) - Method in class org.metaqtl.EMCriteria
  Get the criterion value according to its integer code.
getCriterion(String) - Method in class org.metaqtl.EMCriteria
getCriterion(int) - Method in class org.metaqtl.EMResult
getCriterion() - Method in class org.metaqtl.MetaQtlModel
getCriterionIdx(String) - Static method in class org.metaqtl.EMCriteria
  Returns the integer code for the criterion which matches the given name.
getCritValues(String, int[]) - Method in class org.metaqtl.MetaQtlResult
getCritWeights(String, int[]) - Method in class org.metaqtl.MetaQtlResult
getCrossDesign(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
  This routine returns an object which handle the properties of the offspring which have been used to create the genetic map.
getCrossType() - Method in class org.thalia.bio.entity.CrossPopulation
getCrossType() - Method in interface org.thalia.bio.IBioCross
getCSIdx(int, int) - Method in class org.metaqtl.CMarkerSequence
getDataPoints(int, boolean) - Method in class org.metaqtl.MetaQtlData
  For a given trait group indice this methods returns the data points as a matrix of Double X[0..1][0..n-1] where X[0] is the vector of the n position values and X[1] is the vector of the n standard deviations of the positions.
getDF() - Method in interface org.metaqtl.numrec.NumericalUtilities.Function
  Returns the derivative of the function.
getDF() - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction
  Returns the value of the derivate in x;
getDist() - Method in class org.metaqtl.TreeNode
getDistance(int, int, int) - Method in class org.metaqtl.Chromosome
  This methods returns the distance between the first marker and the marker with the given indice using the given mapping context.
getDistance(int) - Method in class org.metaqtl.Chromosome
  This methods returns the distance between the first marker and the marker with the given indice using the default mapping context.
getDistanceBetween(int, int, int, int) - Method in class org.metaqtl.Chromosome
  This methods returns the distance between the markers with the given indices assuming that `mrkIdxL < mrkIdxR`.
getDistanceBetween(int, int) - Method in class org.metaqtl.Chromosome
getDistHeterogeneity(int, int[][], Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome
getEMEps() - Method in class org.metaqtl.algo.QtlClustAlgorithm
getEMRanStartNumber() - Method in class org.metaqtl.algo.QtlClustAlgorithm
getEuclidean() - Method in class org.metaqtl.EMResult
getF() - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction
  Returns the value of the function in x.
getFirstCommonMrkIdx(Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome
getFunction() - Method in class org.thalia.bio.entity.Ontology
getFunction() - Method in interface org.thalia.bio.IBioOntology
  Returns the function of the ontology
getGeneration() - Method in class org.thalia.bio.entity.Population
getGeneration() - Method in interface org.thalia.bio.IBioCross
getGenome() - Method in class org.thalia.bio.entity.LocusContainer
getGenome() - Method in interface org.thalia.bio.IBioLGroup
getGraph() - Method in class org.metaqtl.ChromCluster
getGroup() - Method in class org.thalia.bio.entity.AlleleContainer
getGroup(String) - Method in class org.thalia.bio.entity.GroupContainer
getGroup() - Method in class org.thalia.bio.entity.Locus
getGroup(String) - Method in interface org.thalia.bio.IBioGenome
getGroup() - Method in interface org.thalia.bio.IBioLocus
getGroups() - Method in class org.thalia.bio.entity.bean.GeneticMapBean
getHeight() - Method in class org.metaqtl.graph.ChromAxe
getHeight() - Method in class org.metaqtl.graph.ChromLayer
getHeight() - Method in class org.metaqtl.graph.GraphShape
getHeight() - Method in class org.metaqtl.graph.Layer
getHeight() - Method in class org.metaqtl.graph.MetaGraph
getHeight() - Method in class org.metaqtl.TreeNode
getHeigth() - Method in class org.metaqtl.graph.QtlShape
getID() - Method in class org.thalia.bio.entity.OntologyTerm
getID() - Method in interface org.thalia.bio.IBioOntologyTerm
  Returns the id if the terms.
getImage(ChromGraph[]) - Static method in class org.metaqtl.graph.GraphFactory
getIndividual(String) - Method in class org.thalia.bio.entity.IndividualContainer
getIndividual(String) - Method in interface org.thalia.bio.IBioPopulation
getIndividualNumber() - Method in class org.thalia.bio.entity.IndividualContainer
getIndividualNumber() - Method in class org.thalia.bio.entity.Population
getIndividualNumber() - Method in interface org.thalia.bio.IBioPopulation
getInstance() - Static method in class org.thalia.bio.util.BioEntityNameComparator
getInstance() - Static method in class org.thalia.bio.util.LocusPositionComparator
getK() - Method in class org.metaqtl.EMResult
getK(MetaSimuStat.SimuConfig[], String) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getKValues() - Method in class org.metaqtl.MetaQtlResult
getLabelSide() - Method in class org.metaqtl.graph.ChromShape
getLayer(double, double) - Method in class org.metaqtl.graph.QtlLayerBuffer
  Returns a QtlLayer which represent the contents of the buffer.
getLeaf(int) - Method in class org.metaqtl.Tree
getLeafHeights() - Method in class org.metaqtl.Tree
getLeafNumber() - Method in class org.metaqtl.Tree
getLeftCSMarker(int, int) - Method in class org.metaqtl.CMarkerSequence
  Returns the indices of the marker at the left of the given one.
getLocus() - Method in class org.thalia.bio.entity.bean.LGroupBean
getLocus(String) - Method in class org.thalia.bio.entity.LocusContainer
getLocus() - Method in interface org.thalia.bio.IBioAllele
getLocus(String) - Method in interface org.thalia.bio.IBioLGroup
getLocusAdapter() - Static method in class org.thalia.bio.entity.Locus
getLocusNumber() - Method in class org.thalia.bio.entity.LocusContainer
getLocusNumber() - Method in interface org.thalia.bio.IBioLGroup
getLocusType() - Method in class org.thalia.bio.entity.Marker
getLocusType() - Method in class org.thalia.bio.entity.QTL
getLocusType() - Method in interface org.thalia.bio.IBioLocus
getMahalanobis(double[]) - Method in class org.metaqtl.EMResult
getMap(IBioGenome[], String) - Static method in class org.metaqtl.main.MetaMain
getMapName() - Method in class org.metaqtl.Chromosome
getMappingCross(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
getMappingFunction(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
  This methods returns the integer code of the mapping function associated to the given genetic map.
getMappingUnit(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
getMarkerDico() - Method in class org.metaqtl.ChromCluster
getMarkerDico() - Method in class org.metaqtl.MapCluster
getMarkerIdx(int, int, int) - Method in class org.metaqtl.CMarkerSequence
getMarkerIdxWithName(String) - Method in class org.metaqtl.Chromosome
  This method looks if it exists a marker on the chromosome with the given name and returns its indice.
getMarkerIndexByName(String) - Method in class org.metaqtl.ChromCluster
  For a given marker name this method returns the marker index of the marker table if found.
getMarkerIntervalNumber() - Method in class org.metaqtl.ChromCluster
  This method returns the total number of marker intervals, i.e the sum over chromosomes of the number of marker intervals.
getMarkerName(String) - Method in class org.metaqtl.ChromCluster
  This method returns the name of the locus from the given name.
getMarkerName(int) - Method in class org.metaqtl.Chromosome
  Returns the names of the marker at the i^th position on the chromosome.
getMarkerNameByIndex(int) - Method in class org.metaqtl.ChromCluster
  This method returns the name of the marker according to this indice.
getMarkerNumber() - Method in class org.metaqtl.ChromCluster
  This method returns the number of distinct markers implied in this cluster, i.e the size of the marker table.
getMarkerOccurence(int) - Method in class org.metaqtl.ChromCluster
  Returns the number of times the marker with the indice i has been seen over the chromosomes of the cluster.
getMetaOccurence(IBioLocus) - Static method in class org.metaqtl.util.LocusProperties
getMetaQtl(String, String, int) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the meta Qtl for the given chromosome indice `cidx`, the given trait name `trait` and the given number of clusters `k`.
getMetaQtl(int) - Method in class org.metaqtl.MetaQtlResult
getMetaQtls() - Method in class org.metaqtl.Chromosome
getModel(String, String) - Method in class org.metaqtl.MetaQtlModel
getModel(int, int) - Method in class org.metaqtl.MetaQtlModel
getMrkTickPoint2D(int, boolean) - Method in class org.metaqtl.graph.ChromLayer
getMrkTickPoint2D(int, boolean) - Method in class org.metaqtl.graph.ChromShape
getMrkToRm(File) - Static method in class org.metaqtl.main.MetaMain
getMu(int) - Method in class org.metaqtl.EMResult
getMu(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getName() - Method in class org.metaqtl.ChromCluster
  Returns the name of the cluster.
getName() - Method in class org.metaqtl.Chromosome
  Returns the name of the chromosome.
getName() - Method in class org.metaqtl.Qtl
  Returns the name of the QTL.
getName() - Method in class org.metaqtl.TreeNode
getName() - Method in class org.thalia.bio.entity.bean.BioEntityBean
getName() - Method in class org.thalia.bio.entity.bean.PropertyBean
getName() - Method in class org.thalia.bio.entity.BioEntity
getName() - Method in class org.thalia.bio.entity.BioEntityCollection
getName() - Method in interface org.thalia.bio.IBioEntity
  Returns the name of the biological entity
getNodeHeights() - Method in class org.metaqtl.Tree
getNodeNumber() - Method in class org.metaqtl.Tree
getO(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getOption() - Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
getOptionChar() - Method in exception org.metaqtl.main.CmdLineParser.NotFlagException
getOptionName() - Method in exception org.metaqtl.main.CmdLineParser.UnknownOptionException
getOptionValue(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser
  Equivalent to `getOptionValue(o, null)`.
getOptionValue(CmdLineParser.Option, Object) - Method in class org.metaqtl.main.CmdLineParser
getOptionValues(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser
getPalette(int) - Static method in class org.metaqtl.graph.PaletteColor
  Returns a palete of colors which should be distinct.
getPaletteGradient(int, Color, Color) - Static method in class org.metaqtl.graph.PaletteColor
getParent() - Method in class org.metaqtl.TreeNode
getParent() - Method in class org.thalia.bio.entity.BioEntity
getParent() - Method in class org.thalia.bio.entity.BioEntityCollection
getParent() - Method in interface org.thalia.bio.IBioEntity
  Returns the entity that handles this entity.
getParents() - Method in class org.thalia.bio.entity.CrossPopulation
getParents() - Method in class org.thalia.bio.entity.Individual
getParents() - Method in class org.thalia.bio.entity.Population
getParents() - Method in interface org.thalia.bio.IBioCross
getParents() - Method in interface org.thalia.bio.IBioIndividual
  Returns the pedigree of the individual
getParentTerm() - Method in class org.thalia.bio.entity.OntologyTerm
getParentTerm() - Method in interface org.thalia.bio.IBioOntologyTerm
  Returns the parent of the term.
getPartNames() - Method in class org.metaqtl.QtlPartition
getPedigree() - Method in class org.thalia.bio.entity.Individual
getPi(int) - Method in class org.metaqtl.EMResult
getPopulation() - Method in class org.thalia.bio.entity.Individual
getPopulation() - Method in interface org.thalia.bio.IBioIndividual
getPosition() - Method in class org.thalia.bio.entity.AlleleContainer
getPosition() - Method in class org.thalia.bio.entity.Locus
getPosition() - Method in interface org.thalia.bio.IBioLocus
getPredict(MetaSimuStat.SimuConfig[], String) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getProba() - Method in class org.metaqtl.Chromosome
getProbaColor(double) - Static method in class org.metaqtl.graph.MetaGraphPar
getProbaColor(double, double) - Static method in class org.metaqtl.graph.MetaGraphPar
getProperties() - Method in class org.thalia.bio.entity.bean.BioEntityBean
getProperties() - Method in class org.thalia.bio.entity.BioEntity
getProperties() - Method in class org.thalia.bio.entity.BioEntityCollection
getProperties() - Method in interface org.thalia.bio.IBioEntity
  Gets the properties of the entity.
getQtl(int, int) - Method in class org.metaqtl.MetaQtlData
  Returns the j^th QTL in the i^th cluster.
getQtlIdx(int) - Method in class org.metaqtl.MetaQtlData
  Returns the indices of the Qtl for the given trait cluster indice `i`.
getQTLInMrkIntProb(int, int, int) - Method in class org.metaqtl.Chromosome
  This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL indice.
getQTLInMrkIntProb(int, int, Qtl) - Method in class org.metaqtl.Chromosome
  This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL.
getQtlNumber() - Method in class org.metaqtl.Chromosome
getQtlNumber() - Method in class org.metaqtl.MetaQtlData
getQtlPartition(Chromosome, IBioOntology) - Static method in class org.metaqtl.main.MetaMain
getQtlPartition(Chromosome, MetaQtlAnalysis, String, int, char) - Static method in class org.metaqtl.main.MetaMain
getQtlPartNames() - Method in class org.metaqtl.graph.QtlPartitionLayer
getQtls() - Method in class org.metaqtl.Chromosome
  This method returns a copy of the QTL located on thic chromosome.
getQTLSD(Qtl.QTLSupport, int, int) - Static method in class org.metaqtl.Qtl
  Depending on the CI type this methods returns the the standard deviation of the QTL position using the given mapping context.
getQTLSD(double, Qtl.QTLCross, int) - Static method in class org.metaqtl.Qtl
  Depending on the r-square parameter and the cross design this method returns the standard deviation of the QTL position for the given mapping context.
getQtlTree() - Method in class org.metaqtl.MetaQtlResult
getRecHeterogeneity(int, int[][], Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome
getRemainingArgs() - Method in class org.metaqtl.main.CmdLineParser
getResources(IResource, IBioEntity[]) - Static method in class org.thalia.bio.util.ResourceBioEntityQuery
getResult() - Method in class org.metaqtl.algo.ClustAlgorithm
  When the algorithm is finished use this method to get the result.
getResult() - Method in class org.metaqtl.algo.MetaMapAlgorithm
getResult() - Method in class org.metaqtl.algo.QtlProjAlgorithm
getResult(String, String) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the result for the given trait name or null if not found.
getResult(String) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the first result for the given chromosome.
getResult(int, String) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the result for the given trait name or null if not found.
getResults(String) - Method in class org.metaqtl.MetaQtlAnalysis
getRightCSMarker(int, int) - Method in class org.metaqtl.CMarkerSequence
getRoot() - Method in class org.metaqtl.Tree
getRoot() - Method in class org.thalia.bio.entity.Ontology
getRoot() - Method in interface org.thalia.bio.IBioOntology
  Returns the root of the ontology tree.
getSD(int) - Method in class org.metaqtl.EMResult
getSD1(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getSD2(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getSize() - Method in class org.thalia.bio.entity.Population
  Returns the size of the population.
getSize() - Method in interface org.thalia.bio.IBioCross
getSubChromosome(String[]) - Method in class org.metaqtl.Chromosome
getSuboption() - Method in exception org.metaqtl.main.CmdLineParser.UnknownSuboptionException
getSynonymous(String) - Method in class org.metaqtl.MetaDico
getTerm(String) - Method in class org.metaqtl.MetaDico
getTerm(IBioOntologyTerm) - Method in class org.thalia.bio.entity.Ontology
getTerm(String) - Method in class org.thalia.bio.entity.Ontology
getTerm(IBioOntologyTerm) - Method in interface org.thalia.bio.IBioOntology
  Returns if exists the term in the ontology which matches the given one.
getTerm(String) - Method in interface org.thalia.bio.IBioOntology
  This method looks into the ontology if there is a term with the given name and returns it.
getTerms() - Method in class org.metaqtl.MetaDico
getTraitClusterName(int) - Method in class org.metaqtl.MetaQtlData
getTraitClusterNames() - Method in class org.metaqtl.MetaQtlData
  Returns the names of the trait clusters.
getTraitClusterNumber() - Method in class org.metaqtl.MetaQtlData
  Returns the number of trait groups for this data set as defined by the clustering method.
getTraitClusterSize(int) - Method in class org.metaqtl.MetaQtlData
  Returns the size of the trait cluster i.
getTraitIdx(int, String) - Method in class org.metaqtl.MetaQtlAnalysis
getTraitName() - Method in class org.metaqtl.MetaQtlResult
  Returns the name of the trait cluster for this result.
getTraitNames(String) - Method in class org.metaqtl.MetaQtlModel
getTraitNames(int) - Method in class org.metaqtl.MetaQtlModel
getType() - Method in class org.thalia.bio.entity.AlleleContainer
getType() - Method in class org.thalia.bio.entity.BioEntity
getType() - Method in class org.thalia.bio.entity.BioEntityCollection
getType() - Method in class org.thalia.bio.entity.CrossPopulation
getType() - Method in class org.thalia.bio.entity.GeneticMap
getType() - Method in class org.thalia.bio.entity.GroupContainer
getType() - Method in class org.thalia.bio.entity.Individual
getType() - Method in class org.thalia.bio.entity.IndividualContainer
getType() - Method in class org.thalia.bio.entity.LGroup
getType() - Method in class org.thalia.bio.entity.LocusContainer
getType() - Method in class org.thalia.bio.entity.Marker
getType() - Method in class org.thalia.bio.entity.Ontology
getType() - Method in class org.thalia.bio.entity.OntologyTerm
getType() - Method in class org.thalia.bio.entity.Population
getType() - Method in class org.thalia.bio.entity.QTL
getType() - Method in interface org.thalia.bio.IBioEntity
  There are 2 main class of entities.
getType() - Method in interface org.thalia.bio.IBioLocus
getType() - Method in class org.thalia.bio.util.EstimatedLocusPosition
getType() - Method in interface org.thalia.bio.util.ILGroupPosition
getType() - Method in class org.thalia.bio.util.LGroupPosition
getType() - Method in class org.thalia.bio.util.StaticLocusPosition
getUSD(EMResult, int, int, String) - Method in class org.metaqtl.MetaQtlResult
getValue() - Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
getValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option
getValue() - Method in class org.thalia.bio.entity.bean.PropertyBean
getVLabels() - Method in class org.metaqtl.ChromCluster.ClusterGraph
getWidth() - Method in class org.metaqtl.graph.ChromLayer
getWidth() - Method in class org.metaqtl.graph.GraphShape
getWidth() - Method in class org.metaqtl.graph.Layer
getWidth() - Method in class org.metaqtl.graph.MetaGraph
getWidth() - Method in class org.metaqtl.graph.QtlShape
getWorkAmount() - Method in class org.metaqtl.algo.MetaAlgorithm
getWorkAmount() - Method in interface org.metaqtl.IMetaAlgorithm
  Returns the amount of the work to do.
getWorkProgress() - Method in class org.metaqtl.algo.MetaAlgorithm
getWorkProgress() - Method in interface org.metaqtl.IMetaAlgorithm
  Returns the amount of work which have already been done.
getX() - Method in class org.metaqtl.graph.AnchoredElement
getX() - Method in class org.metaqtl.graph.ChromAxe
getX() - Method in class org.metaqtl.TreeNode
getX(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
getXBestPred() - Method in class org.metaqtl.EMResult
getXChrom() - Method in class org.metaqtl.graph.ChromShape
getXPred() - Method in class org.metaqtl.EMResult
getXPredIdx(int) - Method in class org.metaqtl.EMResult
getY() - Method in class org.metaqtl.graph.AnchoredElement
getY() - Method in class org.metaqtl.TreeNode
getYDistance(QtlShape, QtlShape) - Static method in class org.metaqtl.graph.QtlShape
  Computes the distance between two Qtl shapes assuming along the same axe Y (i.e the shapes have same X).
getYMax() - Method in class org.metaqtl.graph.ChromAxe
getYMax() - Method in class org.metaqtl.graph.ChromLayer
getYMax() - Method in class org.metaqtl.graph.ChromShape
getYMax() - Method in class org.metaqtl.graph.GraphShape
getYMax() - Method in class org.metaqtl.graph.Layer
getYMax() - Method in class org.metaqtl.graph.QtlLayer
getYMax() - Method in class org.metaqtl.graph.QtlPartitionLayer
getYMax() - Method in class org.metaqtl.graph.QtlShape
getYMax() - Method in class org.metaqtl.graph.QtlTreeLayer
getYMin() - Method in class org.metaqtl.graph.ChromAxe
getYMin() - Method in class org.metaqtl.graph.ChromLayer
getYMin() - Method in class org.metaqtl.graph.ChromShape
getYMin() - Method in class org.metaqtl.graph.GraphShape
getYMin() - Method in class org.metaqtl.graph.Layer
getYMin() - Method in class org.metaqtl.graph.QtlLayer
getYMin() - Method in class org.metaqtl.graph.QtlPartitionLayer
getYMin() - Method in class org.metaqtl.graph.QtlShape
getYMin() - Method in class org.metaqtl.graph.QtlTreeLayer
getZ(int) - Method in class org.metaqtl.EMResult
GraphFactory - Class in org.metaqtl.graph
GraphFactory() - Constructor for class org.metaqtl.graph.GraphFactory
GraphShape - Class in org.metaqtl.graph
GraphShape() - Constructor for class org.metaqtl.graph.GraphShape
group - Variable in class org.metaqtl.Qtl.QTLTrait
  The name of the group to which the trait belongs.
GroupContainer - Class in org.thalia.bio.entity
  Class Description Here
GroupContainer() - Constructor for class org.thalia.bio.entity.GroupContainer
GroupContainer(String, IBioEntity) - Constructor for class org.thalia.bio.entity.GroupContainer
groupNumber() - Method in class org.thalia.bio.entity.GroupContainer
groupNumber() - Method in interface org.thalia.bio.IBioGenome
groups - Variable in class org.thalia.bio.entity.bean.GeneticMapBean
groups() - Method in class org.thalia.bio.entity.GroupContainer
groups() - Method in interface org.thalia.bio.IBioGenome
gser(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities

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